[BioC] microRNA microarray analysis

[Kasper Daniel Hansen]

On Oct 16, 2007, at 5:23 AM, Philipp Pagel wrote:

>
>> I am analyzing two color microarrays with limma but I am getting  
>> blank
>> and empty spots as differentially expressed genes in topTable. I have
>> made spot files but can't get get rid of them.
>
> You can use logical subsetting of your MA or RG object. E.g.  you  
> could
> use something like
>
> RG = RG$genes$Status = controlStatus(spottypes, RG)
> RGnoblanks = RG[!(RG$gene$Status %in% c('blank','empty')), ]
>
> The only catch with this is that somehow the color attribute seems to
> get lost in the process, resulting in a surprise the next time you use
> plotMA(). But you can fix this by re-doing the controlStatus step.  
> (BTW:
> does anybody here know why the color attribute is dropped?)

Because attributes gets dropped when you do the limma-based  
subsetting. Someone would have to implement a attribute-preserving  
subsetting method.

Kasper


> The other side of the story is, that blank spots should not appear  
> to be
> differntially expressen in the first place...
>
> cu
> 	Philipp
>
> -- 
> Dr. Philipp Pagel                              Tel.  +49-8161-71 2131
> Lehrstuhl für Genomorientierte Bioinformatik   Fax.  +49-8161-71 2186
> Technische Universität München
> Wissenschaftszentrum Weihenstephan
> 85350 Freising, Germany
>
>  and
>
> Institut für Bioinformatik / MIPS
> GSF - Forschungszentrum für Umwelt und Gesundheit
> Ingolstädter Landstrasse 1
> 85764 Neuherberg, Germany
> http://mips.gsf.de/staff/pagel
>
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